Review of Bacteriology &

Clinical Microbiology
Prof. Md. Akram Hossain
April, 2011
 Aetiology of diarrhoea in Bangladesh
Agent All ages < 5 yrs
E. coli 34.9% 43.6%
Rotavirus 23.7 % 37.9%
V. Cholerae O1 22.9 % 12.7%
Campylobacter jejuni 9.5% 11.0%
Shigella spp. 6.0% 5.6%
Salmonella 2.0% 1.6%
E. histolytica 1.2 % 0.3%
Giardia lamblia 1.6% 0.8%
Cryptosporidium 0.7% 1.1%
No Pathogen 19.6% 17.5%
Mixed pathogen 31.6% 36.0%
Prof. Akram, Review Systemic Microbiology 2
 Bacterial aetiology
Sl Agent Sl. Agent
1. Esch coli 2 Shigella spp.
(ETEC, EPEC, EHEC..)
3. Salmonella spp. 4. Vibrio cholerae

5. Campylobacter jejuni 6. Yersinia Enterocolitica

7. Staphylococcus aureus 8. Bacilus cereus

9. Clostridum perfringens 10. Clostridum difficile

Prof. Akram, Review Systemic Microbiology 3

 Viral Etiology of diarrhoeae…
Sl no. Agent Comment
1. Rota virus Commonest,
Watery, among children
2. Norwalk virus

3. Calici virus

4. Adenovirus

5. Astrovirus

Prof. Akram, Review Systemic Microbiology 4

Protozoal aetiology of diarrhoea …
Sl no. Agent Comment

1. E. histolytica Invasive

2. Giardia lamblia Non invasive

3. Cryptosporidium Immunosuppressed
parvum
4. Balantidium coli Immunosuppressed

Prof. Akram, Review Systemic Microbiology 5

Mechanisms involved in diarrhoea

Invasion of GIT
Salmonella, Shigella, Campylobacter, Escherichia
coli, and Entamoeba histolytica.
histolytica.
Non invasive
Toxin production
Vibrio cholerae, ETEC
Decreased absorption
rotavirus, norwalk agent, giardia lamblia

Prof. Akram, Review Systemic

Microbiology 6
14.. Name the causative agents causing
14
meningitis according to different age
group.. Briefly describe the pathogenesis of
group
gonorrhoea.

Prof. Akram, Review Systemic

Microbiology 7
 Aetiology of meningitis -1
Bacteria Age group
Streptococcus Gr.B Newborn
Esch. Coli Newborn
Listeria monocytogenes Newborn
H. Influenzae Children > 6 months
S. Pneumoniae Young adult
N. Meningitidis Adult
Staphylococci Adult
Other GNB Adult

Prof. Akram, Review Systemic

Microbiology 8
 Aetiology of meningitis -2
Protozoa Age group
Acanthamoeba Any age
Naegleria fowleri Adult
Plasmodium falciparum Any age
fungi
Cryptococcus neoformans Immunocompromised
Virus Adult
Polio Any age
Arboviruses Meningo encephalitis

Prof. Akram, Review Systemic

Microbiology 9
 Lab Dx of Meningitis

Principle: is based on Cytology & biochemical test of CSF

(Sugar & Protein), demonstration of the CA from CSF by M/E and
culture ( cell culture in case of virus) and also by Ag detection.
Steps:
•Specimen : CSF & Blood
•M/E : TC & DC of WBC of uncentrifuged & Gram stained
smear of centrifuged smear.
•Isolation & identification (Culture): In BA, CA,MA
370C aerobically for 24-48 hrs, cell culture for viral infections.
•Immunological test : Detection of bacterial antigens & Ag
of C.neoformans from CSF by LAT or other tests.
•Special tests: CSF sugar & protein, India Ink for C. neoformans.

Prof. Akram, Review Systemic Microbiology 10

15..
15 Name the causative agents of
nongonococcal urethritis.
urethritis. Write down
the mechanism of action of cholera
toxin..
toxin

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Microbiology 11
 Aetiology of NGU
1. Chlamydia trachomatis
2. Mycoplasma hominis
3. Mycoplasma genitalium
4. Ureaplasma urealyticum
5. Trichomonas vaginalis
6. Candida albicans

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Microbiology 12
 Mechanism of action of Cholera toxin
Cholera toxin

Binds with intestinal epithelial cells by B subunit

A subunit enters into cells & activates adenyl cyclase

Increases concentration of cAMP within cells

Hypersecretion of water & chlorides and inhibition of reabsorption

of sodium.

Intestinal lumen is distended with fluid & there is hypermotility

leading to profuse diarrhea.
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Microbiology 13
1. Enumerate important toxins and
enzymes of Streptococcus pyogenes.
pyogenes.
Give the pathogenesis of Rheumatic
fever..
fever

Prof. Akram, Review Systemic

Microbiology 14
Toxins of Streptococcus pyogenes
Streptolysin ‘O’ – Oxygen labile, has
antigenicity.. Destructs RBCs, ASO rises following
antigenicity
streptococcal sore thora but not skin infections
infections..
Streptolysin ‘S’ – Oxygen stable, Not antigenic
antigenic..
Pyrogenic toxin (Erythogrnic toxin) A –
Present in few strains which are lyosogenic and
responsible for scarlet fever.
fever.
Pyrogenic toxin (Erythogrnic toxin) B -
Rapidly destroys tissue and responsible for necrotizing
fascitis
Prof. Akram, Review Systemic
Microbiology 15
 Enzymes of Streptococcus pyogenes
1. Hyaluronidase (Spreading factor) factor)-- Breaks
down proteoglycans of Connective tissuetissue..
2. Streptokinase (Fibrinolysin) – activates
plasminogen to plasmin that breaks fibrin clot clot..
3. DNase (Streptodornase) – depolymerizes
DNA in exudates or necrotic tissue.
tissue. Antigenic.
Antigenic.
4. C5-a peptidase - degrades complement component of
C5a, which attracts phagocytes to the sites of complement
deposition..
deposition Prevents chemotaxis of neutrophils and
mononuclear phagocytes.
phagocytes.

Prof. Akram, Review Systemic

Microbiology 16
 Other Virulence Factors
1. Capsule - antiphagocytic
2. Fc Binding Protein - antiphagocytic
3. M Protein - antiphagocytic, adhesion
4. Plasmin Binding Protein

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Microbiology 17
Pathogenesis of Acute Rheumatic Fever

Nonsuppurative inflammatory lesions involving the:

Heart
Joints
Subcutaneous Tissues
Central Nervous System
Usually follows an upper respiratory infection with
Group A streptococci of certain M protein
serotypes 1, 3, 5, 6, 14, 18, 19, 24
Latency 1-
1-5 weeks (Average 19 days)
Risk after untreated pharyngitis <3%
Cutaneous infections do not
Prof. Akram, Reviewlead to ARF
Systemic
Microbiology 18
Pathogenesis of Acute Rheumatic Fever…

Role of M protein in the pathogenesis is

unclear. Two hypothesis:
1. Due to structural features, M protein elicits the
production of antibodies cross reactive with host
myosin, where type II hypersensitivity reaction is
responsible for tissue damage.
damage.
2. Due to its superantigenic properties, M protein
stimulates many Th cells thereby releasing large
amount of interleukins and thereby causing tissue
damage..
damage
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Microbiology 19
2. Classify Enterobacteriaceae
Enterobacteriaceae.. Write
down the pathogenesis of Enteric
fever..
fever

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Microbiology 20
Classification of Enterobacteriaceae

Clinical classification
Primarily intestinal pathogen
Primarily extra-
extra-intestinal pathogen
Both intestinal and extra-
extra-intestinal
Classification based on lactose fermentation
Lactose fermenters
Lactose non fermenters
Late fermenters

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Microbiology 21
 Clinical classification
Primarily Intestinal Pathogen
1. Shigella 2. Y. enterocolitica
Intestinal & Extraintestinal Pathogen
1. Salmonella 2. Esch. coli
Extra Intestinal pathogen-
pathogen-
1. Klebsiella 2. Proteus 3.Enterobacter
4. Citrobacter 5. Y. pestis etc...

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Classification based on lactose fermentation

Lactose fermenters
1. Esch coli 2. Klebsiella, 3. Enterobacter
4. Citrobacter 5. Serratia
Lactose non fermenters
1. Salmonella 2. Shigella except Sh.sonni 3. Proteus

Late lactose ferments –

1. Sh.sonni 2. Citrobacter 3.Providencia 4. Serratia

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Microbiology 23
Pathogenesis of enteric fever
Salmonella typhi, paratyphi A, B, C

Small intestine

Attach, invade epithelial cells & engulfed by MPS where they multiply

Released into blood via thoracic duct– Primary bacterimia

7 -10 days

Cleared from blood by MPS and will lodge in liver, spleen, lung, Lymph node

Parasitized cells undergoes necrosis & bacilli heavily reinvade blood

Secondary heavy bacterimia Clinical illness
Occurs at 14th days
Localized to gall bladder, liver, spleen etc of infection

From gallbladder to payers patches of Review

Prof. Akram, intestine-hemorrhage,
Systemic Microbiology ulcer 24
 First time
2nd time

Pathogenesis of typhoid fever

Prof. Akram, Review Systemic Microbiology 25
3. Write down the virulence factors of Neisseria
gonorrhoeae with their role in pathogenesis
pathogenesis.. How
can you diagnose acute gonococcal urethritis in
the laboratory?

Prof. Akram, Review Systemic

Microbiology 26
Virulence factors of N. gonorrhoeae
Pilli – the most important virulence factor which
mediate attachment to the mucosal cell surface
and antiphagocyatic.
Ig A protease-
protease- destroy secretory IgA
Lipooligosaccharide (LOS) of cell wall – like
endotoxin
Outer membrane proteins (OMP)–
(OMP)–
/antigenic variation in pilli and OMPs -
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Microbiology 27
What are the virulence factors of N. gonorrhoeae?
Virulence factors of N.gonorrhoeae
N.gonorrhoeae--
1. Pilli –
Adherence to target epithelial cells
Resistance to phagocytosis
2. Lipooligosaccharides –
– endotoxin
3. Outer membrane proteins (OMPs 1&2)
– OMP 1 - Adherence to target epithelial cells
– OMP--2 – porines
OMP
4. IgA1 protease
– cleaves IgA1 that defends mucosal surface.
5. Fbp (iron binding protein)
Prof. Akram, Review Systemic Microbiology 28
 Lab diagnosis of gonococcal urethritis
Principle: Diagnosis of gonococcal urethritis is based on
Principle:
Gram staining and culture of the dischage. dischage.
Immunological test are not helpful because of antigenic
variation, NA based tests are useful
Steps
Specimen : Urethral discharge
M/E : Gram Stained smear is very sensitive and specific is
adequate for diagnosis in male.
male.
Culture: Chocolate agar or Thayer –Martin media is
Culture:
needed to be incubated at 370C for 24
24--48 hrs.
hrs. Immediate inoculation of
discharge in media is needed
needed..
PCR : of urine samples are widely used as screening test.
test.
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Microbiology 29
4. Classify Mycobacterium
Mycobacterium.. Write down
the interpretation of tuberculin test
test..

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Microbiology 30
 How can you classify Mycobacteria?

1. Mycobacterium tuberculosis complex which can cause

tuberculosis::
tuberculosis
1. M. tuberculosis,
2. bovis,
M. bovis,
3. africanum,,
M. africanum
4. M. microti and M. canetti.
canetti.
2. M. leprae which causes Hansen's disease or leprosy. leprosy.
3. Nontuberculous mycobacteria (NTM (NTM)) also known as
atypical mycobacteria or opportunistic mycobacteria
are all the other mycobacteria which can cause
pulmonary disease resembling tuberculosis,
lymphadenitis, skinProf.disease, or disseminated disease.
Akram, Review Systemic
disease.
Microbiology 31
 Classification of Mycobacterium ..
Runyon classification - Ernest Runyon in 1959 classified in 4
groups
Photochromogens, which develop pigments in or after being exposed to
light.. M. kansasii,
light kansasii, and M. marinum.
marinum.
Scotochromogens, which become pigmented (orange to yellow) in
Scotochromogens,
darkness / light
light.. M. scrofulaceum
Non-chromogens,
Non- chromogens, which includes a group of prevalent opportunistic
pathogens called M. avium complex (MAC) M. ulcerans,
ulcerans, M. xenopi,
xenopi, M.
malmoense,, , M. haemophilum and M. genavense.
malmoense genavense.
Rapid growers rapidly growing non-
non-chromogenic species
species:: M. chelonae,
chelonae, M.
abscessus,, M. fortuitum
abscessus

No. of NTM rises from about 50 in 1997 to over 125 by January

No.
2007
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Microbiology 32
 Mantoux test
100 years old test.test. Used to see whether a
person is exposed to M.tuberculosis naturally or
artificially . It does not indicate a person is
suffering from disease or immune to disease.
disease.
5 TU PPD is injected into upper skin layer
of the patient's arm.
arm.
The arm is examined 48 to 72 hours
Any swelling that can be felt around the site
of the injection, also known as induration, is
measured
Interpretation--
Interpretation
Positive - > 10 mm-
mm- due to disease, or BCG
Negative -< 10 mm – No exposure
False positive – Positive without disease due
to atyptical mycobacteria
False negative-
negative- Negative with disease e.g.
Milliary TB, Immunosuppression due to
Prof. Akram, Review Systemic
AIDS, cytotoxic drugs etc
etc.. Microbiology 33
 Lab Diagnosis of Tuberculosis
Principle:
Lab diagnosis of TB is based on demonstration of AFB
by microscopy (LM & FM), isolation by culture,
culture,
Immunological tests ( Ab & Cell mediated), Nucleid
acid based techniques (PCR & Probes)
Probes)..

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Microbiology 34
Lab diagnosis of TB…Microscopy

Microscopy - Microscopy is the easiest and most rapid

diagnostic procedure that detect the acid fast bacilli in clinical
specimen..
specimen

It is less sensitive than culture and requires high bacillary load

5,000 to 10
10,,000
000/ml
/ml..

its sensitivity varies from 30

30%
% to 70
70%
%. Its sensitivity can be
increased up to 74 – 78 78%
% when centrifuged concentrated
deposited are used

Three type of staining are used (i) Ziehl-

Ziehl-Neelsen stain (ii)
(ii)
Fluorochrome stain and (iii) Kinyoun stain
Prof. Akram, Review Systemic
Microbiology 35
Lab diagnosis of TB…Culture
culture provides the definitive diagnosis of tuberculosis
defending on the decontamination method and the type of
culture medium used, as few as 10 to 100 viable tubercle
bacilli/ml of sample can be detected.
detected.

EGG-BASED MEDIA -Dorset media (1903

EGG- 1903),
), Lowenstein
Lowenstein--
Jensin media (1930),
1930), Ogawa media (1949) 1949)
AGAR BASED MEDIUM -Middlebrook 7H – 10 , 7H – 11
INCUBATION - at 350 to 370C until growth is observed or
discarded as negative after 8 weeks.
weeks.
LIQUID MEDIA – Dubos media, Sula media – 10 days
required for growth.
MGIT – Mycobactyerial growth indicator tube
RADIOMETRIC METHOD BACKTEC 460 TB Method
Prof. Akram, Review Systemic
(Beckton Dickinson) 5-5- 7 days Microbiology 36
Lab diagnosis of TB…Immunological
Both T Cell based and antibody based immunological
tests are available
T cell based -
TUBERCULIN SKIN TEST
(1) Mantoux test and
(2) Heaf test.
Quantiferon--TB
Quantiferon
Antibody based –
ENZYME LINKED IMMUNOSORBENT ASSAY (ELISA) –
38 kDa protein, Antigen A-
A-60,
IMMUNOCHROMATOGRAPHY (ICT)

Prof. Akram, Review Systemic

Microbiology 37
Ques:: How you will you proceed to diagnose a case of pulmonary
Ques
tuberculosis ?
Ans::
Ans
Principle :
Diagnosis of PTB is based on demonstration of the AFB by Z-N
& Fluorescent stained smear, then isolation & identification of by
culture, and detection of Antibody or DTHby immunological tests.
tests.
detection of genes by NA based techniques are also used.
used.
Steps::
Steps
Specimen : Sputum, gastric lavage in infants& blood for serology
M/E : Z-N Stained smear or rhodamine –auramine stained smear
Isolation & identification (Culture)
(Culture):: For PTB
PTB-- sputum is to be cultured in
special media like L.J and is to be incubated at 370C aerobically for 4-6 weeks),
BACTEC, MGIT
Immunological tests : ICT, ELISA for Ab and MT, Quantiferon for CMI
NA based techniques : PCR

Prof. Akram, Review Systemic

Microbiology 38
5. Name five indications of blood culture
culture..
Why blood culture done in the 1st and
Widal test in 2nd week of Typhoid fever
fever--
explain..
explain

Prof. Akram, Review Systemic

Microbiology 39
Indications of blood culture

1. Septicemia
2. Sepsis
3. Meningitis
4. Enteric fever
5. Endocarditis

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Microbiology 40
How blood culture differs from other
cultures?
1. Liquid media (broth) is required
2. Amount of sample (Blood) is more 5-5-10
ml ( other e.g. CSF, Urine etc only 1-
1-2
drops)
3. More than 1 sample is to be cultured
4. Timing of collection is important

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Microbiology 41
 Types of blood culture
1. Traditional blood culture
• Broth culture or biphasic culture
2. Lytic centrifugation method
3. Automated blood culture
culture--continuous-
continuous-
monitoring blood culture systems
(CMCCS).

Prof. Akram, Review Systemic

Microbiology 42
 How to collect the blood for culture?
Ten ml (milliliter) of blood is usually needed for each blood
culture bottle.
bottle. (1:10 proportion)
First locates a vein in the inner elbow region
region.. The area of skin
where the blood will be drawn must be disinfected by wiping the
area with alcohol in a circular fashion,
The same pattern of wiping is repeated using an iodine or
iodophor solution.
solution.
The top of the bottle is disinfected using alcohol.
alcohol.
Draw the blood and about 10 ml of blood is injected into each
blood culture bottle.
bottle.
The type of bottles used will vary based on whether the
physician is looking for bacteria (aerobes or anaerobes), yeast,
mold, or viruses
viruses..

Prof. Akram, Review Systemic

Microbiology 43
6. Enumerate some coccobacilli.
coccobacilli. Name the clinical
conditions produce by H. influenzae type b. How
can you prevent H. influenzae type b infection in
children?

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Microbiology 44
Clinically important coccobacilli
1. Haemophilus,
2. Legionella,
3. Bordetella

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Microbiology 45
 Diseases caused by H.influenzae
Type b Unencapsulated
Meningitis Otitis Media
CSF 50%-95% culture positive Tymphanocentesis
Blood 50%-95% culture positive 50% - 70% culture positive

Conjunctivitis Sinusitis
Eye 50%-75% culture positive Sinus aspirate
Blood < 10% culture positive 50% - 75% culture positive

Cellulitis Pneumonia, bronchitis

Skin 75% - 90% culture positive Sputum
Blood 50% - 75% culture positive 20% - 75% culture positive
Blood
10% - 30% culture positive
Epiglottitis
Blood 90% - 95% culture positive
Epiglottitis culture
contraindicated

Arthritis
Synovial fluid
70% - 90% culture positive
Blood
50% - 80% culture positive

Prof. Akram, Review Systemic Microbiology 46

Prevention of H.influenzae

Vaccination against Hib

There are several types of Hib conjugate
vaccines available for use use.. All of the vaccines are
approved for use in children 15 months of age and older
and some are approved for use in children beginning at 2
months of age
age.. More than 90
90%% of infants obtain long term
immunity with 2-3 doses of the vaccine
vaccine..
All children should have a vaccine approved for infants
beginning at 2 months.
months.
All unvaccinated children 15 - 59 months old should receive a
single dose of conjugate vaccine.
vaccine.
Children 60 months of age or older and adults normally do not
need to be immunized.
immunized.

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Microbiology 47
Virulence factors of H. influenzae

1. Capsule:: The polyribosyl ribitol phosphate (PRP) capsule is the

Capsule
most important virulence factor because it renders type b H. influenzae
resistant to phagocytosis by polymorphonuclear leukocytes
leukocytes..
2. Fimbriae increase the adherence of bacteria to human mucosal cells in
vitro, and they are required for successful colonization of the
nasopharynx..
nasopharynx
3. Neuraminidase and an IgA protease
protease,, are produced by all
virulent strains, though role in pathogenesis is unclear
unclear..
4. Endotoxin in meningitis or bacteremia is unclear,
5. outer membrane lipooligosaccharide is thought to play a role in
inflammation associated with otitis media
media..

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Microbiology 48
 Classification of Haemophilus

Haemophilus belongs to family Pasteurellaceae

Pasteurellaceae..
Clinically important species
H. influenzae
Meningitis, otitis media, epiglotitis, pneumonia etc
H. parainfluenzae
H. ducreyi
Chancroid
H. aegyptius
Conjunctivitis

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Microbiology 49
Classification of Haemophilus influenzae

Haemophilus influenzae-
influenzae-
Uncapsulated
normal flora of URT & noninvasive disease
Capsulated
Polysaccharide capsule responsible for invasiveness
There are six serotypes based on antigenicity of capsular
polysaccharide..
polysaccharide
These are a, b, c, d, e, f
Of the 6 serotypes, only H. influenmzae type b is responsible
for most of the invasive diseases (Hib), and vaccine is
available only against Hib
Hib..

Prof. Akram, Review Systemic Microbiology 50

7. Name five Rickettsial diseases with vectors
vectors..
Write down the pathogenesis of Peptic ulcer
disease caused by H. pylori
pylori..

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Microbiology 51
 Rickettsial diseases with vectors
Rickettsia prowazekii - Epidemic typhus - body
louse = bite/feces
Rickettsia rickettsii - Rocky Mountain spotted fever
tick bite
Rickettsia tsutsugamushi-
tsutsugamushi- Scrub typhus mite
bite
Rickettsia tyhi-
tyhi- endemic typhus flea
Rochalimaea quintana - Trench fever
body louse bite/feces

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Microbiology 52
 Pathogenesis of H.pylori
Stomach acid

H.pylori lives in the mucus lining to

escape from the highly acidic gastric
juice.. (Its helical shape facilitates its
juice
penetration of the mucus layer.
layer.)
It can fight the acid by excreting an
enzyme called urease
urease..

Gastric epithelium
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Microbiology 53
 Pathogenesis of H.pylori
Stomach acid

The immune system responds to the

infection by sending white cells, killer T
cells, and other infection fighting agents
agents..
However, they cannot easily get through
stomach lining to reach the infection.
infection.
As the immune response grows, immune
cells die and release destructive
compounds on the stomach lining cells cells..
Within a few days, gastritis and perhaps
eventually a peptic ulcer results.
results.

Gastric epithelium
Prof. Akram, Review Systemic Microbiology 54
 Virulence factors of H.pylori
Adhesion
Colonization factors
Urease
Phospholipase A & B
Responsible for destruction of the protective mucous zone
Loss of this protective barrier allows the stomach acid and
digestive enzymes to have direct access to the gastric
epithelium..
epithelium
Toxins-- Cytotoxins
Toxins

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Microbiology 55
 How To Diagnose H pylori
• Invasive tests (biopsy through endoscope)
Rapid Urease Test (RUT)
Culture
Histology
Polymerase Chain Reaction (PCR)

• Non--Invasive tests
Non
Urea Breath Tests (UBT)
Serological tests
13C bicarbonate assay
Salivary assay
Urine
Stool antigen testsProf. Akram, Review Systemic
Microbiology 56
Which bacteria is associated with Peptic Ulcer Disease
(PUD)? How can you diagnose in the lab? What is the
treatment?

Helicobacter pylori is associated with following PUD.

Gastric and Duodenal ulcers
Chronic superficial gastritis (Type B)
Associated with increased risk of gastric carcinoma
Lab diagnosis is by based on
isolation of the bacteria from gastric biopsy,
Rapid urease test
Serology for detection of antibody
Culture of the bacteria requires in special media (Campy BAP, Skirrows
etc) at 42 0C in microaerophilic environment.
Treatment by triple antibiotic therapy-
therapy-Amoxicillin,
metronidizole or tetracycline, and bismuth
Prof. Akram, Review Systemic Microbiology 57
16. Write down the peculiarities of Pseudomonas and
16.
Mycoplasma.. Give the salient feature of UTI
Mycoplasma
caused by Proteus
Proteus..

Prof. Akram Hossain, Review Systemic Microbiology 58

Salient properties of Pseudomonas
Pseudomonads are Gram-Gram-negative rods, obligate
aerobe, motile.
motile.
They are clinically important because
they are resistant to most antibiotics
Widely distributed in soil and water, human gut (10
10%%)
diverse metabolic capabilities
many can grow in distilled water to >106 per ml
growth on wide range of carbon sources
readily available for nosocomial infections
Susceptible to drying, airborne spread less likely
They also produce a slime layer that is resistant to
phagocytosis.
Prof. Akram, Review Systemic Microbiology 59
Salient properties of Mycoplasma
Smallest free-
free-living bacteria, Pleomorphic
filaments .1-.3 um in diameter, No cell wall, Cell
membrane contains sterols.
sterols.
Mycoplasmas are facultative aerobes, Require
sterols in medium, Grow slowly, upto 3 weeks
may require.
require. Small colonies ,"fried egg" colonies
on agar plates

Prof. Akram Hossain, Review Systemic Microbiology 60

8. Classify Vibrios
Vibrios.. Write down the lab
diagnosis of pulmonary tuberculosis
tuberculosis..

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Microbiology 61
Classification of Toxigenic V. cholerae
Toxigenic V. cholerae
Division into 2 epidemic serotypes

O1
Division into 2 biotypes O139

Classical El Tor
Each O1 biotype can have 3 serotypes

inaba ogawa hikojima

Division into ribotypes

A&B
A&C A, B, C
(A little C) Antigens

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Microbiology 62
 V. Cholerae classfication
Vibrionaceae

Vibrio

V. cholerae V. parahemolyticus V. vulnificus V. fluvialis V. mimicus

“O” serotype >150

O-1, Non O-1, O-139-V.cholearebengal,

Pnademic & Mild diarrhea Pnademic & epidemic
epidemic cholera
cholera
Three serotypes; Ogawa, Inaba,
Hikojima Prof. Akram, Review Systemic
Two biovars; classic and El TorMicrobiology 63
 Virulence factors of V.cholerae O1 and O139
Virulence factor Biological effect
*** Cholera toxin Hypersecretic of electrolytes and water

Coregulated pilus Adherence to mucosal cells adhesin

Accessory colonization factor adhesin

Hemagglutination protease Releases bacteria from mucosal cells

Zona occludens Exotoxin

Accessory cholera enterotoxin Exotoxin
Flagellum Motility

Siderophores Iron sequestration

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Microbiology 64
 Lab diagnosis of cholera
Principle: Demonstration of organism
Principle:
by M/E ( DGI), Isolation/
identification in special culture, Ag
detection from stool
stool..

Prof. Akram Hossain, Review Systemic Microbiology 65

Lab Diagnosis of cholera

M/E: Organism can be seen in stool by dark field

illumination (DGI).
Culture: Monsurs medium (TTGA), and TCBS
agar plate.
immunological methods: Quick, Ag detection –
from stool

Serotyping tests are available to define

strains, but this is needed only during
epidemics to trace the source of infection.

Prof. Akram, Review Systemic Microbiology 66

 Why V. cholerae is important in our
country?
V. cholerae is important for following reasons
1. V. cholerae causes cholera which is endemic and
epidemic in our country.
country.
2. One strain O-139 is known as V. cholerae Bengal.
Bengal.
3. One media for is discovered by Bangladeshi scientist
Professor KA Monsur (Mansurs media) for cultivation
of this bacteria.
bacteria.
4. Robert Koch visited Calcutta to examine the stool of
cholera patients
5. ORS is discovered at ICDDRB, Dhaka
Dhaka..

Prof. Akram Hossain, Review Systemic Microbiology 67

9. Enumerate the causes of sexually
transmitted diseases
diseases.. Write down the
lab diagnosis of syphilis in a newborn
baby..
baby

Prof. Akram, Review Systemic

Microbiology 68
What are common causes of STD?
Bacterial (all are GNB)
1. N.gonorrhoeae 2. T.pallidum
3. Chlamydia trachomatis D -K - NGU
4. Chlamydia trachomatis L1,L2,L3 - LGV
5. Calymmatobacterium granulomatis - GI
6. H. ducrey - Chancroid
7. Mycoplasma - NGU
8. Gardnerella vaginalis
Viral
1. Papilloma virus 2. Herpes simplexvirus-
simplexvirus-2
3. HIV 4. HBV
Protozoal
1. Trichomonas vaginalis
Fungal
1. Candida albicans
Others
1. Sarcoptis scabiei 2. Phthirus pubis
Prof. Akram, Review Systemic
Microbiology 69
 Lab diagnosis of newborn syphilis
Principle: Lab diagnosis of newborn syphilis or
Principle:
congenital syphilis is based on detection of Anti
T.P IgM antibody or rising titer of VDRL.
VDRL.
Steps::
Steps
Specimen : Blood
Immunological tests:tests: FTAIgMAbs test,
Determination of titer of VDRL of Mother
and Newborn
Newborn.. If it more than mother and
rising then it diagnostic
diagnostic..

Prof. Akram Hossain, Review Systemic Microbiology 70

10..
10 What do you mean by antibiotic
associated diarrhea? Write down the
pathogenesis of tetanus
tetanus..

Prof. Akram Hossain, Review Systemic Microbiology 71

 Pathogenesis of tetanus -1

Tetanus is caused by Clostridium tetani, which is distributed in the

soil and in the feces of horses and other animals.
animals.
C tetani is not an invasive organism.
organism. The infection remains strictly
localized in the area of devitalized tissue (wound, burn, injury,
umbilical stump, surgical suture) into which the spores have been
introduced..
introduced
Germination of the spore and development of vegetative
organisms that produce toxin are aided by (1) necrotic tissue, (2)
calcium salts, and (3) associated pyogenic infections, all of which
aid establishment of low oxidation
oxidation--reduction potential
potential..
The vegetative cells of C tetani produce the toxin tetanospasmin
(MW 150150,,000)
000)
The toxin initially binds to receptors on the presynaptic
membranes of motor neurons.
neurons. It then migrates by the retrograde
axonal transport system to the cell bodies of these neurons to the
spinal cord and brain stem.
stem.

Prof. Akram Hossain, Review Systemic Microbiology 72

 Pathogenesis of tetanus -2

The toxin diffuses to terminals of inhibitory cells,

including both glycinergic interneurons and aminobutyric
acid--secreting neurons from the brain stem.
acid stem.
The toxin degrades synaptobrevin, a protein required for
docking of neurotransmitter vesicles on the presynaptic
membrane..
membrane
Release of the inhibitory glycine and -aminobutyric acid
is blocked, and the motor neurons are not inhibited.
inhibited.
Hyperreflexia, muscle spasms, and spastic paralysis result.
result.
Extremely small amounts of toxin can be lethal for
humans..
humans

Prof. Akram Hossain, Review Systemic Microbiology 73

11. Name the diarrhoeagenic strains of
11.
coli. Write down the lab diagnosis of
E.coli.
UTI caused by E. coli
coli..

Prof. Akram, Review Systemic

Microbiology 74
 Diarrhoeagenic Esch coli
Different types of diarrhoea & dysentery are caused different
strains of Esch coli.
1. EPEC - Infantile, Watery diarrhoea in developing
countries
2. ETEC – Travellers, watery diarrhoea
3. EHEC – Bloody diarrhoea
VTEC – Haemolytic uremic syndrome
4. EIEC - Shigella like dysenetry
5. Entero adherent (EAdEC) –Acute & Chronic
diarrhoea in children
6. Enteroaggregative E. coli (EAggEC)-
(EAggEC)-– Persistent diarrhoea

Prof. Akram, Review Systemic

Microbiology 75
Lab Dx of Urinary tract infection
Principle: Is diagnosed by M/E & semi-quantitative culture of
urine.
Steps:
•Specimen : Clean catch MSU or Supra pubic puncture in Infants
•M/E : Wet preparation of centrifuged deposit helps in provisional
diagnosis (Pus cells present > 05/HPF is significant)
•Culture: measured amount of urine (.001 -.002 ml) is
inoculated by calibrated loop in general purpose media like BA, MA
and is incubated at 370C aerobically for overnight. Colony count-
105/ml for GNB is significant. Identification is done by standard
biochemical tests.
•Immunological test : Not used

Prof. Akram, Review Systemic Microbiology 76

Lab Diagnosis of diff types Esch coli infections

Principle : In case of extraintestinal infections isolation

and identification from the clinical samples is enough
but in case of Intestinal infections, furthers tests are
required to identify different Enetropathogenic
strains--
strains
E.g.
EPEC – Serotyping, ETEC – rabbit ileal loop or
ELISA
VTEC – Serotyping
EAEC & EAggEC – in special cell lines (tissue
culture)
EIEC – By seryne’s test, Hep-
Hep-2 cells
Prof. Akram, Review Systemic
Microbiology 77
12.. Write down five important zoonotic
12
diseases with their causative organism
organism..
Give the laboratory diagnosis of leprosy.
leprosy.

Prof. Akram, Review Systemic

Microbiology 78
 Lab diagnosis of leprosy
Principle: Based on demonstration of AFB by
modified acid fast staining from slit skin
smear. Lepromin test is used for staging
the disease.
Steps:
1. collection of specimen- slit skin smear
2. Microscopy – modified Z-N stain decolorizing
by 5% sulphuric acid or 1% HCL.
3. Culture – no role
4. Lepromin test – for staging of disease.
Diseases and infections which are naturally
transmitted between vertebrate animals and
humans (WHO)
There are 1,407 known human disease pathogens 816
(58
58%
%) are zoonotic diseases

Prof. Akram, Review Systemic

Microbiology 80
 Zoonoses: Bacterial Examples
Anthrax* Plague*
Brucellosis* Psittacosis*

Campylobacteriosis* Q fever*
Cat--scratch disease*
Cat Relapsing fevers
Leptospirosis* Salmonellosis*
Listeriosis* Tularemia*
Lyme disease* Yersiniosis
Prof. Akram, Review Systemic
* indicates covered in lectures Microbiology 81
 Zoonoses: Viral Examples
Colorado tick fever Japanese encephalitis
Ebola Monkeypox*
Equine encephalitides Nipah*
(WEE, EEE, VEE)
Hantaviruses Rabies*
Hendra* Rift Valley fever
Herpesvirus B West Nile virus*
Influenza Yellow fever
Prof. Akram, Review Systemic
* indicates covered in lectures Microbiology 82
 Zoonoses: Parasitic Examples
PROTOZOAL HELMINTHIC
Trypanosomiasis Baylisascariasis*
Babesiosis Cysticercosis
Cryptosporidiosis* Hydatidosis
Leishmaniasis Schistosome dermatitis
Giardiasis* Trichinosis*
Toxoplasmosis* Visceral larva migrans and
toxocariasis*
Prof. Akram, Review Systemic
* indicates covered in lectures Microbiology 83
Zoonoses: Mycotic Examples

Aspergillosis
Blastomycosis
Cryptococcosis*
Dermatophytosis*
Histoplasmosis
Sporotrichosis

Prof. Akram, Review Systemic

Microbiology 84
13..
13 Enumerate obligate intracellular
bacteria.. How can you diagnose a case
bacteria
of Chlamydia trachomatis infection in
the laboratory?

Prof. Akram, Review Systemic

Microbiology 85
 Lab Diagnosis of Chlamydia trachomatis
Principle: Based on cytological test for detection of
inclusion bodies, culture in cell line, detection of Ag
and Ab and also DNA based tests
Cytology
Iodine-staining
Iodine- Iodine-stained inclusion bodies
inclusions
Not as sensitive
Culture
In McCoy cell lines.
Iodine staining
inclusions
Most specific

Prof. Akram, Review Systemic

Microbiology 86
 C. trachomatis – Diagnosis…
Antigen detection (ELISA or IF)
Group specific LPS
Strain specific outer membrane proteins
Antibody detection (ELISA or IF)
Can’t distinguish between current or past infection
Detection of high titer IgM antibodies can be helpful
Nucleic acid probes
PCR
May eventually replace culture
Prof. Akram, Review Systemic
Microbiology 87
 Classification of Chlamydiaceae

Genus: Chlamydia
C. trachomatis - Urogenital infections, trachoma,
conjunctivitis, pneumonia and lymphogranuloma
venerium (LGV)
Genus: Chlamydophilia
C. psittaci - Pneumonia (psittacosis)
C. pneumoniae - Bronchitis, sinusitis, pneumonia
and possibly atherosclerosis

N.B. New taxonomy, previously three species in one genus - Chlamydia

Prof. Akram, Review Systemic
Microbiology 88
 Chlamydia-- special properties
Chlamydia
Small obligate intracellular parasites
Small genome (~600 genes)
1/6 the size of E. coli
lacks many essential metabolic genes
Contain DNA, RNA and ribosomes
Inner and outer membrane
LPS but no peptidoglycan
Cell wall not well characterized
Energy parasites
Can’t make ATP

Prof. Akram, Review Systemic

Microbiology 89
 Special properties
Can not be cultured in artificial media
Must cultivate on eukaryotic host cells
embryonated chicken eggs
McCoy cells in monolayer tissue cultures
-mouse brains
Has
Elementary and Reticulate bodies

Prof. Akram, Review Systemic

Microbiology 90
 Chlamydia trachomatis & Human Disease
15 serovars
Serovars A, B, Ba, C Conjunctivitis (trachoma)
Serovars B, D to K Urethritis
Cervicitis
Proctitis
Pelvic inflammatory disease
Epididymitis
Conjunctivitis
Neonatal pneumonitis
Reactive arthritis
Serovars L1, L2, L3 Lymphogranuloma venereum
(ulcers, lymphadenopathy,
Prof. Akram,strictures,
Review Systemic proctitis)
Microbiology 91
Chlamydial Development

http://www.chlamydiae.com/images/devcycpan.GIF

Prof. Akram, Review Systemic Microbiology 92

Steps of Lab Dx of bacterial diseases
Specimen : According to site of infection (Sputum
blood, stool, urine, swab etc)
M/E : Stained (G S/ Z-N/ Albert) or unstained
preparation or DGM or IFM
Isolation & identification (Culture): media, incubation
time, temp & environment should be mentioned -( For
PTB- sputum is to be cultured in special media like L.J and is to be
incubated at 370C aerobically for 4-6 weeks)
Immunological tests : ICT, ELISA for Ab
NA based techniques : PCR

Prof. Akram, Review Systemic Microbiology 93

To know how to suggest is
the art of teaching
Amiel

Prof. Akram, Review Systemic Microbiology 94

Ques: How can you classify Streptococcus.
Ans: There many pathogenic species. So, classification is
Complex. Following are some important classifications.
Based on Oxygen requirement :
Obligate anaerobe : Peptostreptococcus
Facultative anaerobe : Most of the streptococci
Based on Hemolysis in BA : (Brown 1919)
Beta hemolytic : Most pathogenic spp. eg. Str. pyogenes
Alpha hemolytic : Str. viridans, Str. pneumonae
Gamma hemolytic : Str. fecalis, Enterococci, etc.
Based on Group and Type specific cell wall antigen
Grouping based on cell wall CHO antigen : (Lancefield 1933) There 19
Groups – A B C D E F G H K L M N O P Q R S T U V of which
Group A, B, C, D, & G are human pathogens
Typing based on cell wall M protein antigen : (Griffith )
Strains of Strep. Gr A are further typed into >80 serotypes, Some are
rheumatogenic and some are nephrotigenic.

Prof. Akram, Review Systemic Microbiology 95

What are the post-streptococcal diseases
AGN & RF
Which one is type II and which one is type III
hypersensitivity mediated?
• AGN -III, RF -II

What is the clinical significance of Strep Gr B & Gr D

Strep Gr. B causes neonatal meningtis & Gr D causes UTI which is
frequently drug resistant.
Why Strep Gr. B causes neonatal meningitis? What is the
other cause? How can you prevent it?
Esch coli. Due to vaginal carriage. Prophylactic ampicillin.

Prof. Akram, Review Systemic Microbiology 96

Q: Enumerate the diseases caused by Staphylococcus aureus.
Answer: Diseases can be described under the following headings.
Direct invasion :
Pneumonia – Secondary to viral URTI .
Meningitis -
Osteomyelitis (in children)
Acute bacterial endocarditis
Septic arthritis ( Children and old age group >50 yrs)
Skin infections –
Impetigo, Cellulitis, Boil, furuncle, carbuncle, wound infections.
Bacterimia / septicemia
Urinary tract infection
Exotoxin dependant :
Gastroenteritis (food poisoning)- Rapid onset of vomiting and diarrhoea with
rapid recovery.
Toxic shock syndrome – Due to TSST-1 which stimulate TNF and IL-1 and
characterised by High fever, Nausea /vomiting, Diarrha, Erythematous rash,
Hypotension, Desquamation of palms and soles
Scalded skin syndrome

Prof. Akram, Review Systemic Microbiology 97

No man can be a good teacher unless be has
feelings of warm affection towards his pupils and
a genuine desire to impart to them what he
himself believes to be of value.
Bertrand Russel

Prof. Akram, Review Systemic Microbiology 98

 Enumerate the virulence factors of Staph aureus with their
pathogenicity ?
Virulence factors of Staph aureus
Factors that disable immune defenses:
Protein A - Binds with Fc portion of Ig G, may protect from opsonization and
phagocytosis.
Coagulase – Leads to fibrin formation & protects from phagocytosis.
Hemolysins – ( 4 types): Alpha, beta, gamma and delta. They destroy RBC, Neutrophils,
Macrophages and Platelets.
Leukocoidins – They destroy leukocytes
Penicillinase – Desrupts Beta lactam ring penicillins.
Tissue destroying factors :
Hyaluronidase (Spreading factor)- Braks down proteoglycans of Connective tissue.
Staphylokinase – lyses formed fibrin clots
Lipase – Degrades fats and oils of skin and facillitates S.aureus colonization of
sebaceous glands.
Exotoxins :
Exfoliatin- Causes the skin to slough off (S S S)
Enterotoxins (Heat stable):
Toxic shock syndrome toxin (TSST-1) : Similar to pyogeinc toxin of Strptococcus
pyogenes. And causes toxic shock syndrome.

Prof. Akram, Review Systemic Microbiology 99

16. Enumerate the important exotoxin-
producing bacteria. Write in short the
pathogenesis of Anthrax.

Prof. Akram, Review Systemic Microbiology 100

 Important toxin producing bacteria
1. Vibrio cholerae
2. Corynebacterium diphtheriae
3. Clostrdium tetani
4. Clostrdium botulinum
5. Streptococcus pyogenes
6. Staphylococcus aureus
7. ETEC

Prof. Akram, Review Systemic Microbiology 101

Pathogenesis of anthrax
Anthrax is caused by Bacillus anthracis. In humans,
approximately 95% of cases are cutaneous anthrax and 5% are
inhalation. Gastrointestinal anthrax is very rare.
Cutaneous anthrax generally occurs on exposed surfaces of the
arms or hands, followed in frequency by the face and neck. A
pruritic papule develops 1–7 days after entry of the organisms
or spores through a scratch. Initially it resembles an insect bite.
The papule rapidly changes into a vesicle or small ring of
vesicles that coalesce, and a necrotic ulcer develops. The
lesions typically are 1–3 cm in diameter and have a
characteristic central black eschar.

Prof. Akram, Review Systemic Microbiology 102

How can you classify the family Enterobacteriaceae?
Clinical classification-
Primarily Intestinal Pathogen
• Shigella
Intestinal & Extraintestinal Pathogen -
1. Salmonella 2. Esch. coli
Extra Intestinal pathogen-
1. Klebsiella 2. Proteus 3.Enterobacter 4. Citrobacter etc...
Classification based on lactose fermentation-
Lactose fermenters (LF)-
1. Esch coli 2. Klebsiella, 3. Enterobacter 4. Citrobacter
5. Serratia
Lactose non fermenters (NLF)-
1. Salmonella 2. Shigella except Sh.sonni 3. Proteus
Late lactose ferments –
1. Sh.sonni 2. Citrobacter 3.Providencia 4. Serratia

Prof. Akram, Review Systemic Microbiology 103

Education is a progressive discovery of our own
ignorance.
Will Durant (1885 - 1981)

Prof. Akram, Review Systemic Microbiology 104

What are the Diseases caused by Klebsiella, Proteus,
Enterobacter, citrobacter, serratia etc
UTI
Septicaemia
Meningitis
Nosocomial infections
Name the diseases caused by Esch coli
UTI
Gastroenteritis by enteric pathogenic strains (EPEC, ETEC,
EIEC etc)
Others
Name the diseases caused by Salmonella ?
S. typhi, S.Paratyphi A,B,C - Enteric fever
S. cholera suis - septicaemia
S.enteritidis - gastrotenteritis
Prof. Akram, Review Systemic Microbiology 105
Q. What is enteric fever? Why it is so called? Name
tests used for diagnosis in the 1st week of illness.

Ans: Enetric fever is a systemic illness, manifested by

fever and other symptoms and caused by
Salmonella typhi, S. paratyphi A, S. paratyphi B, &
S. paratyphi C. They are so called because their
main lesion occurs in the intestine ( payers
patches).
Blood culture and detection of salmonella antigen from
the blood and other specimens are the reliable tests
used for diagnosis in the first week of illness.
Prof. Akram, Review Systemic Microbiology 106
Lab Dx of Enteric fever
Principle: is based on isolation of the Salmonella spp. by blood culture
also by immunological test i.e. detection of antibody (widal test) and
antigen (recently introduced). Tests of choice varies with duration of
illness. Blood culture and antigen detection is reliable in the fist week and
widal test is helpful in 2nd week onwards.
Steps:
Specimen : Blood for culture in 1st week and for
serological test in 2nd week..
M/E : is not helpful.
Isolation & identification (Culture): Blood culture can be
done in three processes -
Traditional - using liquid media or biphasic media
Lytic method - after processing in lytic solution directly in solid media
Automated - very rapid (within 6 hrs)
Immunological test :
Prof. Akram, Review Systemic Microbiology 107
What are anaerobic bacteria? Why they can not tolerate oxygen?
Classify them
Ans:
Anaerobic bacteria are a group of bacteria that do not use oxygen for growth
and metabolism and fail to grow on the surface of solid medium in ambient
air.
They can not tolerate oxygen because they lack following –
Cytochrome systems for the metabolism of oxygen.
Superoxide dismutase
Catalase
Classification
GNB
• Bacteroides fragilis
GPB
• Spore-forming - Clostrdium
• Nonsporeforming – Actinomyces, lactobacilus
GPC- peptostreptococci
GNC - Veilloneilla

Prof. Akram, Review Systemic Microbiology 108

Why is haemophilus so called? Name diseases caused by Hib

Ans:

Haemophilus means blood loving. They require heated blood agar for
their growth so they are called as Haemophilus.
Diseases caused by haemophilus influenzae-b are as follows
Common infections
• Meningitis in children
• Otitis media
• Sinusitis
• Septic arthirtis
Rare infections
• Acute epiglottitis
• Bacteraemia
• Septicaemia
• Endocarditis
Prevention of Hib
Vaccine prepared from capsule

Prof. Akram, Review Systemic Microbiology 109

Which sore throat is acute emergency and which has
long term effect ? What is their pathogenesis?
Sore throat due to C. diphtheriae is an acute emergency
and sore throat due to S. pyogenes long term
complications.
Diphtheria is due to a powerful exotoxin which inhibits
protein synthesis by inhjbiting EF-2
Rheumatic fever is followed by streptococcal sore throat
which is due to cross reaction between streptococcal cell
wall component and myocardial tissue and mediated by
type II Hypersensitivity reaction.

Prof. Akram, Review Systemic Microbiology 110

Can all C. diphtheriae cause diphtheria? Why? How
can you test toxigenicty?

Only toxigenic strains can cause diphtheria,

which due to presence of corynephage with
the bacteria. Non toxigenic strains can cause
pharyngitis.
Toxigencity can be tested by
In vivo- Eleks test
In vitro – Guineapig inoculation test.

Prof. Akram, Review Systemic Microbiology 111

METACHROMATIC GRANULES

Prof. Akram, Review Systemic Microbiology 112

Eleks preciitation test
Prof. Akram, Review Systemic Microbiology 113
Experience teaches only the teachable.
Aldous Huxley (1894 - 1963)

Prof. Akram, Review Systemic Microbiology 114

What is Weil-Felix test? What is the basis of this test? What
is the name of these antibodies?

Weil-Felix test is serological test where Antigens from

proteus spp. are used for detection of antibodies against
some rickettssial disease.

Alkali stable polysaccharide antigen- found in some

rickettsial strains is shared by certain strains of Proteus
spp. is the basis of Weil-Felix reaction

OX19,OX2 and OXK antigens are used to detect

heterophile antibodies.
Prof. Akram, Review Systemic Microbiology 115
Teachers open the door. You enter by
yourself.
Chinese Proverb

Prof. Akram, Review Systemic Microbiology 116

Some easy but tricky questions
Name 5 bacterial diseases
Correct answer
Tuberculosis, Leprosy, Cholera, Syphilis, gonorrhoea
Incorrect answer
Diarrhoea, Dysentery, meningitis etc
Name 5 viral diseases
Correct answer
Measles, Mumps, Rabies, Poliomyelitis, AIDS
Incorrect answer
Diarrhoea, meningitis, encepahilits etc
Prof. Akram, Review Systemic Microbiology 117
Common aetiology
UTI-
Esch coli, klebsiella, Proteus, Pseudomonas, Staph
saprophyticus, Streptococcus Gr D.
Meningitis
N.meningitidis, Strep pneumoniae, Strep. Group B,
H.influenzae, Esch coli.
Diarrhoea
Shigella, Salmonella, Esch coli(ETEC, EPEC, EIEC
etc), Camplyobacter jejuni, V.cholerae, E.histolytica,
Giardia, Rotavirus.

Prof. Akram, Review Systemic Microbiology 118

Common aetiology

•Sore throat
• Mostly viral (85%)(Rhino, Adeno, Corona, Picorna, Influenza,
parainfluenza, Coxackie, EB, HSV )
•Bacterial (15%) - Strep.pyogenes, N.gonorrhoeae, C.diphtheriae
•Septicaemia
• N.meningitidis, Strep pneumoniae, Strep. Group B, H.influenzae,
Esch coli.
•Pneumonia- varies with age
•In children- mostly viral, In adults - bacterial
• Strep. pneumoniae, Klebsiella pneumoniae, Mycoplasma
pneumoniae, Chlamydia, Staph aureus, Esch coli & GNB.

Prof. Akram, Review Systemic Microbiology 119

What are the important causes of Pneumonia ?
Bacterial
1. Streptococcus pneumoniae - 20 -60% (Community)
2. Haemophilus influenzae 05 - 15 % (Community)
3. Mycoplasma pneumoniae (Primary atypical)
4. Chlamydia pneumoniae (Primary atypical)
5. Chlamydia psittaci (Primary atypical)
8. Klebsiella pneumoniae (Hospitalized )
11. Pseudomonas aeroginosa (Cystic fibrosis)
Viral
1. Influenzavirus- Primary viral pneumonia
2. Parainfluenza virus - children < 5 yrs
3. Measles virus 4. RSV
Fungal
1. Pneumocystis carinii - in AIDS pts
2. Aspergillus fumigatus

Prof. Akram, Review Systemic Microbiology 120

What are the microbial causes of Pneumonia ?
Bacterial
1. Streptococcus pneumoniae - 20 -60% (Community)
2. Haemophilus influenzae 05 - 15 % (Community)
3. Mycoplasma pneumoniae (Primary atypical)
4. Chlamydia pneumoniae (Primary atypical)
5. Chlamydia psittaci (Primary atypical)
6. Staphylococcus aureus
7. Legionella pneumophila
8. Klebsiella pneumoniae (Hospitalized )
9. Esch coli (Hospitalized )
10. Serratia (Hospitalized )
11. Pseudomonas aeroginosa (Cystic fibrosis)
12. Bacillus anthracis (Occupational )
13. Coxiella burnetti
Viral
1. Influenzavirus- Primary viral pneumonia
2. Parainfluenza virus - children < 5 yrs
3. Measlesvirus 4. RSV
5. Adenovirus 6. Varicell -zostervirus
7. Cytomegalovirus - Interestitial pneumonia
Fungal Prof. Akram, Review Systemic Microbiology 121
1. Pneumocystis carinii - in AIDS pts
2. Aspergillus fumigatus
Check list (Bacteriology & Cl. Microbiology)

Kochs postulates, Prokaryotes, Eukaryotes, essential and nonessential

structures of bacterial cell, functions of cell wall, CM, Flagella,
fimbria, capsule, spore, Aerobic, Anaerobic, F.anaerobic bacteria
Sterilization, Disinfection, Antisepsis, Autoclave, Hot air oven,
Pasteurization, Tyndalization, chemical sterilizing agents, Growth
curve, Generation time
Virulence factors, exotoxin, Endotoxin, Enetrotoxin, Neurotoxin
antibiotics, drug resistance (mechanism, origin, transfer)
Diseases produced by S.aureus, S.saprophyticus, S.epidermidis, Strep.
pyogenes, Strep.pneumoniae, Strep viridans, Esch coli, Salmonella,
Proteus, Kelbsiella, N. gonorrhoeae
Lab Dx of PTB, Syphilis, Rheumatic fever, Enteric fever, Diphtheria,
Leprosy,
Imprtant causes of UTI, Diarrhoea, Food poisoning, Sore throat, STD,
Septicaemia, Meningitis with lab Dx
Prof. Akram, Review Systemic Microbiology 122
Lab Dx of Diarrheal diseases
Principle: is based on demonstration of the CA by M/E and isolation &
identification by standard bacteriological techniques and also by
immunological tests and some special tests.
•Steps:
•Specimen : freshly passed Stool or rectal swab
•M/E : Saline, Iodine, and Z-N preparation is helpful for Eh, Gl,
Cryptosporidium & nature of diarrhea by PC, Mc, RBC.
•Isolation & identification (Culture): MA, SSA, TCBS,
Campy BA depending on provisional diagnosis to be incubated at
370C aerobically for usual pathogens & at 420C microaerophilic for
Campylobacter
•Immunological test : Detection of rotaviral Ag, C.diffcile toxin
from stool by LAT or other tests.
•Special tests: for ETEC, EPEC, VTEC done in reference lab.
Prof. Akram, Review Systemic Microbiology 123
Rank of Infectious Diseases Cause of Death millions %
Pneumonia (all bugs) 3.745 7.2
Tuberculosis 2.910 5.6
Diarrheal diseases (all bugs) 2.455 4.7
HIV 2.300 4.4
Malaria (falciparum) 1.5-2.7 2.9-5.2
Measles .960 1.8
Hepatitis B .605 1.2
Pertussis .410 0.8
Prof. Akram, Review Systemic Microbiology 124
Principle of Lab Dx of bacterial diseases

Diagnosis of bacterial disease is based on

demonstration of the causative agents by M/E,
then isolation & identification of by culture, and
detection of Antibody or antigen by
immunological tests. In special cases other tests
like toxigenicity tests, detection of genes by NA
based techniques are used.

Prof. Akram, Review Systemic Microbiology 125

Which microbes infects CNS?
Bacteria
Clostridium botulinum
Mycobacterium leprae
Virus
Poliovirus
Rabies virus
Arboviruses
Protozooa
Cryptococcus neoformans
Trypanosoma brucei gambiense
Naegleria fowleri
prions

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Prof. Akram, Review Systemic Microbiology 127
Figure 22.14
The whole art of teaching is only the art of
awakening the natural curiosity of young minds
for the purpose of satisfying it afterwards.
Anatole France (1844 - 1924)

Prof. Akram, Review Systemic Microbiology 128